Error from import cell2location
See original GitHub issueHi, I was just wondering whether anyone could interpret this error or give me any tips how to fix it? I’ve installed cell2location in a conda environment as per the instructions to do so manually but am getting this error upon trying to import it:
In [1]: import sys
...: import scanpy as sc
...: import anndata
...: import pandas as pd
...: import numpy as np
...: import os
...:
...: data_type = 'float32'
...:
...: import cell2location
...:
LoweringError: Failed in nopython mode pipeline (step: nopython mode backend)
Storing i64 to ptr of i32 ('dim'). FE type int32
File "../../../.local/lib/python3.7/site-packages/umap/layouts.py", line 52:
def rdist(x, y):
<source elided>
result = 0.0
dim = x.shape[0]
^
During: lowering "dim = static_getitem(value=$8load_attr.2, index=0, index_var=$const10.3, fn=<built-in function getitem>)" at /home/camerongw/.local/lib/python3.7/site-packages/umap/layouts.py (52)
I’m using python-3.7.10.
Issue Analytics
- State:
- Created 2 years ago
- Comments:7 (4 by maintainers)
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Hi camerongw!
I can’t reproduce this error, but it’s definitely something related to the
numba
package. Are you using the0.53.0
version? Could you please try the following?conda update numba
I would strongly recommend using a separate conda environment for cell2location and other tools you are using.
If you are already doing that your error suggests that python uses
umap
from.local/lib/python3.7/site-packages/umap
rather than conda environment. This is a common error in some HPC and can be solved by disabling the pip user site by adding this line to your.bashrc
:You also need to make sure that you active the conda environment, and that your
$PATH
environmental variable contains path to the conda environment before the path to any other python installation.